-
1
-
-
0000266922
-
A randomization test for phylogenetic information in systematic data
-
Archie JW. 1989. A randomization test for phylogenetic information in systematic data. Syst Zool. 38:219-225.
-
(1989)
Syst Zool
, vol.38
, pp. 219-225
-
-
Archie, J.W.1
-
2
-
-
0002844544
-
Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees
-
Baum BR. 1992. Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon. 41:3-10.
-
(1992)
Taxon
, vol.41
, pp. 3-10
-
-
Baum, B.R.1
-
4
-
-
0033015732
-
Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies
-
Brinkmann H, Philippe H. 1999. Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol Biol Evol. 16:817-825.
-
(1999)
Mol Biol Evol
, vol.16
, pp. 817-825
-
-
Brinkmann, H.1
Philippe, H.2
-
5
-
-
33747375683
-
Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets
-
Burleigh JG, Driskell AC, Sanderson MJ. 2006. Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets. Syst Biol. 55:426-440.
-
(2006)
Syst Biol
, vol.55
, pp. 426-440
-
-
Burleigh, J.G.1
Driskell, A.C.2
Sanderson, M.J.3
-
6
-
-
0034043778
-
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
-
Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17:540-552.
-
(2000)
Mol Biol Evol
, vol.17
, pp. 540-552
-
-
Castresana, J.1
-
7
-
-
0036208071
-
The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa
-
Cavalier-Smith T. 2002. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol. 52:297-354.
-
(2002)
Int J Syst Evol Microbiol
, vol.52
, pp. 297-354
-
-
Cavalier-Smith, T.1
-
8
-
-
10944248427
-
Computing prokaryotic gene ubiquity: Rescuing the core from extinction
-
Charlebois RL, Doolittle WF. 2004. Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res. 14:2469-2477.
-
(2004)
Genome Res
, vol.14
, pp. 2469-2477
-
-
Charlebois, R.L.1
Doolittle, W.F.2
-
9
-
-
33644700003
-
Toward automatic reconstruction of a highly resolved tree of life
-
Ciccarelli FD, Doerks T, von Mering V, Creevey CJ, Snel B, Bork P. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science. 311:1283-1287.
-
(2006)
Science
, vol.311
, pp. 1283-1287
-
-
Ciccarelli, F.D.1
Doerks, T.2
von Mering, V.3
Creevey, C.J.4
Snel, B.5
Bork, P.6
-
10
-
-
16644395866
-
-
Creevey CJ, Fitzpatrick DA, Philip GK, Kinsella RJ, O'Connell MJ, Pentony MM, Travers SA, Wilkinson M, McInerney JO. 2004. Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proc Biol Sci. 271:2551-2558.
-
Creevey CJ, Fitzpatrick DA, Philip GK, Kinsella RJ, O'Connell MJ, Pentony MM, Travers SA, Wilkinson M, McInerney JO. 2004. Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proc Biol Sci. 271:2551-2558.
-
-
-
-
11
-
-
13844250623
-
Clann: Investigating phylogenetic information through supertree analyses
-
Creevey CJ, McInerney JO. 2005. Clann: investigating phylogenetic information through supertree analyses. Bioinformatics. 21:390-392.
-
(2005)
Bioinformatics
, vol.21
, pp. 390-392
-
-
Creevey, C.J.1
McInerney, J.O.2
-
12
-
-
33750810896
-
The tree of one percent
-
Dagan T, Martin W. 2006. The tree of one percent. Genome Biol. 7:118.
-
(2006)
Genome Biol
, vol.7
, pp. 118
-
-
Dagan, T.1
Martin, W.2
-
13
-
-
34247180015
-
The origin of eukaryotes: A reappraisal
-
de Duve C. 2007. The origin of eukaryotes: a reappraisal. Nat Rev Genet. 8:395-403.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 395-403
-
-
de Duve, C.1
-
14
-
-
17744394753
-
Phylogenomics and the reconstruction of the tree of life
-
Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 6:361-375.
-
(2005)
Nat Rev Genet
, vol.6
, pp. 361-375
-
-
Delsuc, F.1
Brinkmann, H.2
Philippe, H.3
-
15
-
-
0033603539
-
Phylogenetic classification and the universal tree
-
Doolittle WF. 1999. Phylogenetic classification and the universal tree. Science. 284:2124-2129.
-
(1999)
Science
, vol.284
, pp. 2124-2129
-
-
Doolittle, W.F.1
-
16
-
-
33847790997
-
Pattern pluralism and the Tree of Life hypothesis
-
Doolittle WF, Bapteste E. 2007. Pattern pluralism and the Tree of Life hypothesis. Proc Natl Acad Sci USA. 104:2043-2049.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 2043-2049
-
-
Doolittle, W.F.1
Bapteste, E.2
-
17
-
-
33645456207
-
Eukaryotic evolution, changes and challenges
-
Embley TM, Martin W. 2006. Eukaryotic evolution, changes and challenges. Nature. 440:623-630.
-
(2006)
Nature
, vol.440
, pp. 623-630
-
-
Embley, T.M.1
Martin, W.2
-
18
-
-
4143093598
-
A genome phylogeny for mitochondria among alpha-Proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes
-
Esser C, Ahmadinejad N, Wiegand C, Rotte C, Sebastiani F, Gelius-Dietrich G, Henze K, Kretschmann E, Richly E, Leister D, Bryant D, Steel MA, Lockhart PJ, Penny D, Martin W. 2004. A genome phylogeny for mitochondria among alpha-Proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol. 21:1643-1660.
-
(2004)
Mol Biol Evol
, vol.21
, pp. 1643-1660
-
-
Esser, C.1
Ahmadinejad, N.2
Wiegand, C.3
Rotte, C.4
Sebastiani, F.5
Gelius-Dietrich, G.6
Henze, K.7
Kretschmann, E.8
Richly, E.9
Leister, D.10
Bryant, D.11
Steel, M.A.12
Lockhart, P.J.13
Penny, D.14
Martin, W.15
-
19
-
-
34547793558
-
The origin of mitochondria in light of a fluid prokaryotic chromosome model
-
Esser C, Martin W, Dagan T. 2006. The origin of mitochondria in light of a fluid prokaryotic chromosome model. Biol Lett. 3:180-184.
-
(2006)
Biol Lett
, vol.3
, pp. 180-184
-
-
Esser, C.1
Martin, W.2
Dagan, T.3
-
20
-
-
33845452848
-
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis
-
Fitzpatrick DA, Logue ME, Stajich JE, Butler G. 2006. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol. 6:99.
-
(2006)
BMC Evol Biol
, vol.6
, pp. 99
-
-
Fitzpatrick, D.A.1
Logue, M.E.2
Stajich, J.E.3
Butler, G.4
-
22
-
-
0024722874
-
+-ATPase: Implications for the origin of eukaryotes
-
+-ATPase: implications for the origin of eukaryotes. Proc Natl Acad Sci USA. 86:6661-6665.
-
(1989)
Proc Natl Acad Sci USA
, vol.86
, pp. 6661-6665
-
-
Gogarten, J.P.1
Kibak, H.2
Dittrich, P.3
Taiz, L.4
Bowman, E.J.5
Bowman, B.J.6
Manolson, M.F.7
Poole, R.J.8
Date, T.9
Oshima, T.10
-
23
-
-
33846551381
-
Biology's next revolution
-
Goldenfeld N, Woese C. 2007. Biology's next revolution. Nature. 445:369.
-
(2007)
Nature
, vol.445
, pp. 369
-
-
Goldenfeld, N.1
Woese, C.2
-
24
-
-
0036593395
-
Ancient phylogenetic relationships
-
Gribaldo S, Philippe H. 2002. Ancient phylogenetic relationships. Theor Popul Biol. 61:391-408.
-
(2002)
Theor Popul Biol
, vol.61
, pp. 391-408
-
-
Gribaldo, S.1
Philippe, H.2
-
25
-
-
0024358140
-
Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes
-
Iwabe N, Kuma K, Hasegawa M, Osawa S, Miyata T. 1989. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci USA. 86:9355-9359.
-
(1989)
Proc Natl Acad Sci USA
, vol.86
, pp. 9355-9359
-
-
Iwabe, N.1
Kuma, K.2
Hasegawa, M.3
Osawa, S.4
Miyata, T.5
-
26
-
-
33645816587
-
Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified
-
Keane TM, Creevey CJ, Pentony MM, Naughton TJ, McInerney JO. 2006. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol. 6:29.
-
(2006)
BMC Evol Biol
, vol.6
, pp. 29
-
-
Keane, T.M.1
Creevey, C.J.2
Pentony, M.M.3
Naughton, T.J.4
McInerney, J.O.5
-
27
-
-
33646726959
-
Genomics and the irreducible nature of eukaryote cells
-
Kurland CG, Collins LG, Penny D. 2006. Genomics and the irreducible nature of eukaryote cells. Science. 312:1011-1014.
-
(2006)
Science
, vol.312
, pp. 1011-1014
-
-
Kurland, C.G.1
Collins, L.G.2
Penny, D.3
-
28
-
-
34247613950
-
Disappearing act
-
Lake JA. 2007. Disappearing act. Nature. 446:983.
-
(2007)
Nature
, vol.446
, pp. 983
-
-
Lake, J.A.1
-
29
-
-
0031513152
-
The average consensus procedure: Combination of weighted trees containing identical or overlapping sets of taxa
-
Lapointe FJ, Cucumel G. 1997. The average consensus procedure: combination of weighted trees containing identical or overlapping sets of taxa. Syst Biol. 46:306-312.
-
(1997)
Syst Biol
, vol.46
, pp. 306-312
-
-
Lapointe, F.J.1
Cucumel, G.2
-
30
-
-
2442581218
-
The importance of proper model assumption in bayesian phylogenetics
-
Lemmon AR, Moriarty EC. 2004. The importance of proper model assumption in bayesian phylogenetics. Syst Biol. 53:265-277.
-
(2004)
Syst Biol
, vol.53
, pp. 265-277
-
-
Lemmon, A.R.1
Moriarty, E.C.2
-
31
-
-
33646360208
-
Selective forces for the origin of the eukaryotic nucleus
-
Lopez-Garcia P, Moreira D. 2006. Selective forces for the origin of the eukaryotic nucleus. Bioessays. 28:525-533.
-
(2006)
Bioessays
, vol.28
, pp. 525-533
-
-
Lopez-Garcia, P.1
Moreira, D.2
-
32
-
-
33748369465
-
The last eukaryotic common ancestor (LECA): Acquisition of cytoskeletal motility from aerotolerant spirochetes in the Proterozoic Eon
-
Margulis L, Chapman M, Guerrero R, Hall J. 2006. The last eukaryotic common ancestor (LECA): acquisition of cytoskeletal motility from aerotolerant spirochetes in the Proterozoic Eon. Proc Natl Acad Sci USA. 103:13080-13085.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 13080-13085
-
-
Margulis, L.1
Chapman, M.2
Guerrero, R.3
Hall, J.4
-
33
-
-
0035197418
-
An overview of endosymbiotic models for the origins of eukaryotes, their ATP-producing organelles (mitochondria and hydrogenosomes), and their heterotrophic lifestyle
-
Martin W, Hoffmeister M, Rotte C, Henze K. 2001. An overview of endosymbiotic models for the origins of eukaryotes, their ATP-producing organelles (mitochondria and hydrogenosomes), and their heterotrophic lifestyle. Biol Chem. 382:1521-1539.
-
(2001)
Biol Chem
, vol.382
, pp. 1521-1539
-
-
Martin, W.1
Hoffmeister, M.2
Rotte, C.3
Henze, K.4
-
34
-
-
2642689666
-
The hydrogen hypothesis for the first eukaryote
-
Martin W, Muller M. 1998. The hydrogen hypothesis for the first eukaryote. Nature. 392:37-41.
-
(1998)
Nature
, vol.392
, pp. 37-41
-
-
Martin, W.1
Muller, M.2
-
35
-
-
30344486571
-
On the desirability of models for inferring genome phylogenies
-
McInerney JO. 2006. On the desirability of models for inferring genome phylogenies. Trends Microbiol. 14:1-2.
-
(2006)
Trends Microbiol
, vol.14
, pp. 1-2
-
-
McInerney, J.O.1
-
36
-
-
13844306928
-
New methods ring changes for the tree of life
-
McInerney JO, Wilkinson M. 2005. New methods ring changes for the tree of life. Trends Ecol Evol. 20:105-107.
-
(2005)
Trends Ecol Evol
, vol.20
, pp. 105-107
-
-
McInerney, J.O.1
Wilkinson, M.2
-
37
-
-
33744982063
-
Time for a change
-
Pace NR. 2006. Time for a change. Nature. 441:289.
-
(2006)
Nature
, vol.441
, pp. 289
-
-
Pace, N.R.1
-
38
-
-
12444313041
-
Identifying and removing fast-evolving sites using compatibility analysis: An example from the Arthropoda
-
Pisani D. 2004. Identifying and removing fast-evolving sites using compatibility analysis: an example from the Arthropoda. Syst Biol. 53:978-989.
-
(2004)
Syst Biol
, vol.53
, pp. 978-989
-
-
Pisani, D.1
-
39
-
-
0036005524
-
Matrix representation with parsimony, taxonomic congruence, and total evidence
-
Pisani D, Wilkinson M. 2002. Matrix representation with parsimony, taxonomic congruence, and total evidence. Syst Biol. 51:151-155.
-
(2002)
Syst Biol
, vol.51
, pp. 151-155
-
-
Pisani, D.1
Wilkinson, M.2
-
40
-
-
0026822436
-
Phylogenetic inference based on matrix representation of trees
-
Ragan MA. 1992. Phylogenetic inference based on matrix representation of trees. Mol Phylogenet Evol. 1:53-58.
-
(1992)
Mol Phylogenet Evol
, vol.1
, pp. 53-58
-
-
Ragan, M.A.1
-
42
-
-
4544313053
-
The ring of life provides evidence for a genome fusion origin of eukaryotes
-
Rivera MC, Lake JA. 2004. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature. 431:152-155.
-
(2004)
Nature
, vol.431
, pp. 152-155
-
-
Rivera, M.C.1
Lake, J.A.2
-
43
-
-
0026684272
-
Evidence that eukaryotes and eocyte prokaryotes are immediate relatives
-
_. 1992. Evidence that eukaryotes and eocyte prokaryotes are immediate relatives. Science. 257:74-76.
-
(1992)
Science
, vol.257
, pp. 74-76
-
-
Rivera, M.C.1
Lake, J.A.2
-
44
-
-
0025736688
-
Cytoskeletal origins in sulfurmetabolizing archaebacteria
-
Searcy DG, Hixon WG. 1991. Cytoskeletal origins in sulfurmetabolizing archaebacteria. Biosystems. 25:1-11.
-
(1991)
Biosystems
, vol.25
, pp. 1-11
-
-
Searcy, D.G.1
Hixon, W.G.2
-
45
-
-
34547820868
-
-
Swofford DL. 1998. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland, Massachusetts
-
Swofford DL. 1998. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland, Massachusetts
-
-
-
-
46
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
47
-
-
0742323538
-
Endosymbiotic gene transfer: Organelle genomes forge eukaryotic chromosomes
-
Timmis JN, Ayliffe MA, Huang CY, Martin W. 2004. Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet. 5:123-135.
-
(2004)
Nat Rev Genet
, vol.5
, pp. 123-135
-
-
Timmis, J.N.1
Ayliffe, M.A.2
Huang, C.Y.3
Martin, W.4
-
48
-
-
22844442070
-
The shape of supertrees to come: Tree shape related properties of fourteen supertree methods
-
Wilkinson M, Cotton JA, Creevey C, Eulenstein O, Harris SR, Lapointe FJ, Levasseur C, McInerney JO, Pisani D, Thorley JL. 2005a. The shape of supertrees to come: tree shape related properties of fourteen supertree methods. Syst Biol. 54:419-431.
-
(2005)
Syst Biol
, vol.54
, pp. 419-431
-
-
Wilkinson, M.1
Cotton, J.A.2
Creevey, C.3
Eulenstein, O.4
Harris, S.R.5
Lapointe, F.J.6
Levasseur, C.7
McInerney, J.O.8
Pisani, D.9
Thorley, J.L.10
-
50
-
-
33847062460
-
Of clades and clans: Terms for phylogenetic relationships in unrooted trees
-
Wilkinson M, McInerney JO, Hirt RP, Foster PG, Embley TM. 2007b. Of clades and clans: terms for phylogenetic relationships in unrooted trees. Trends Ecol Evol. 22:114-115.
-
(2007)
Trends Ecol Evol
, vol.22
, pp. 114-115
-
-
Wilkinson, M.1
McInerney, J.O.2
Hirt, R.P.3
Foster, P.G.4
Embley, T.M.5
-
51
-
-
31344435061
-
Measuring support and finding unsupported relationships in supertrees
-
Wilkinson M, Pisani D, Cotton JA, Corfe I. 2005b. Measuring support and finding unsupported relationships in supertrees. Syst Biol. 54:823-831.
-
(2005)
Syst Biol
, vol.54
, pp. 823-831
-
-
Wilkinson, M.1
Pisani, D.2
Cotton, J.A.3
Corfe, I.4
-
52
-
-
0001271789
-
Phylogenetic structure of the prokaryotic domain: The primary kingdoms
-
Woese CR, Fox GE. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA. 74:5088-5090.
-
(1977)
Proc Natl Acad Sci USA
, vol.74
, pp. 5088-5090
-
-
Woese, C.R.1
Fox, G.E.2
-
53
-
-
0025300402
-
-
Woese CR, Kandler O, Wheelis ML. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria. Eucarya. Proc Natl Acad Sci USA. 87:4576-4579.
-
Woese CR, Kandler O, Wheelis ML. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria. Eucarya. Proc Natl Acad Sci USA. 87:4576-4579.
-
-
-
|